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Yorodumi- PDB-2zze: Crystal structure of alanyl-tRNA synthetase without oligomerizati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zze | ||||||
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Title | Crystal structure of alanyl-tRNA synthetase without oligomerization domain in lysine-methylated form | ||||||
Components | Alanyl-tRNA synthetaseAlanine—tRNA ligase | ||||||
Keywords | LIGASE / hydrolase | ||||||
Function / homology | Function and homology information alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / negative regulation of DNA-templated transcription / zinc ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Sokabe, M. / Ose, T. / Tokunaga, K. / Nakamura, A. / Nureki, O. / Yao, M. / Tanaka, I. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: The structure of alanyl-tRNA synthetase with editing domain. Authors: Sokabe, M. / Ose, T. / Nakamura, A. / Tokunaga, K. / Nureki, O. / Yao, M. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zze.cif.gz | 328.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zze.ent.gz | 269.7 KB | Display | PDB format |
PDBx/mmJSON format | 2zze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/2zze ftp://data.pdbj.org/pub/pdb/validation_reports/zz/2zze | HTTPS FTP |
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-Related structure data
Related structure data | 2zzfC 2zzgC 1riqS 1v7oS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 87989.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: alaS, PH0297, PH0297 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-codonplus-RIL / References: UniProt: O58035, alanine-tRNA ligase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.63 % / Mosaicity: 0.23 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.6 Details: PEG 4000, ammonium acetate, tri-sodium citrate, pH 5.6, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2008 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.9 % / Av σ(I) over netI: 21.41 / Rmerge(I) obs: 0.068 / Χ2: 1.49 / D res high: 2.15 Å / D res low: 50 Å / Num. obs: 100967 / % possible obs: 98.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.15→50 Å / Num. all: 102794 / Num. obs: 100967 / % possible obs: 98.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.068 / Χ2: 1.488 / Net I/σ(I): 21.411 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RIQ, 1V7O Resolution: 2.16→38.58 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.841 / SU B: 9.359 / SU ML: 0.128 / SU R Cruickshank DPI: 0.233 / SU Rfree: 0.187 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Used TLS refinement
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.21 Å2 / Biso mean: 24.6 Å2 / Biso min: 8.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→38.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.157→2.213 Å / Total num. of bins used: 20
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